Anion-Binding Properties of Short Linear Homopeptides.

A comprehensive thermodynamic and structural study of the complexation affinities of tetra (L1), penta (L2), and hexaphenylalanine (L3) linear peptides towards several inorganic anions in acetonitrile (MeCN) and N,N-dimethylformamide (DMF) was carried out. The influence of the chain length on the complexation thermodynamics and structural changes upon anion binding are particularly addressed here. The complexation processes were characterized by means of spectrofluorimetric, 1H NMR, microcalorimetric, and circular dichroism spectroscopy titrations. The results indicate that all three peptides formed complexes of 1:1 stoichiometry with chloride, bromide, hydrogen sulfate, dihydrogen phosphate (DHP), and nitrate anions in acetonitrile and DMF. In the case of hydrogen sulfate and DHP, anion complexes of higher stoichiometries were observed as well, namely those with 1:2 and 2:1 (peptide:anion) complexes. Anion-induced peptide backbone structural changes were studied by molecular dynamic simulations. The anions interacted with backbone amide protons and one of the N-terminal amine protons through hydrogen bonding. Due to the anion binding, the main chain of the studied peptides changed its conformation from elongated to quasi-cyclic in all 1:1 complexes. The accomplishment of such a conformation is especially important for cyclopeptide synthesis in the head-to-tail macrocyclization step, since it is most suitable for ring closure. In addition, the studied peptides can act as versatile ionophores, facilitating transmembrane anion transport.

Overcoming GNA/RNA base-pairing limitations using isonucleotides improves the pharmacodynamic activity of ESC+ GalNAc-siRNAs.

We recently reported that RNAi-mediated off-target effects are important drivers of the hepatotoxicity observed for a subset of GalNAc-siRNA conjugates in rodents, and that these findings could be mitigated by seed-pairing destabilization using a single GNA nucleotide placed within the seed region of the guide strand. Here, we report further investigation of the unique and poorly understood GNA/RNA cross-pairing behavior to better inform GNA-containing siRNA design. A reexamination of published GNA homoduplex crystal structures, along with a novel structure containing a single (S)-GNA-A residue in duplex RNA, indicated that GNA nucleotides universally adopt a rotated nucleobase orientation within all duplex contexts. Such an orientation strongly affects GNA-C and GNA-G but not GNA-A or GNA-T pairing in GNA/RNA heteroduplexes. Transposition of the hydrogen-bond donor/acceptor pairs using the novel (S)-GNA-isocytidine and -isoguanosine nucleotides could rescue productive base-pairing with the complementary G or C ribonucleotides, respectively. GalNAc-siRNAs containing these GNA isonucleotides showed an improved in vitro activity, a similar improvement in off-target profile, and maintained in vivo activity and guide strand liver levels more consistent with the parent siRNAs than those modified with isomeric GNA-C or -G, thereby expanding our toolbox for the design of siRNAs with minimized off-target activity.

Crystallization Pathways of FABr-PbBr2-DMF and FABr-PbBr2-DMSO Systems: The Comprehensive Picture of Formamidinium-Based Low-Dimensional Perovskite-Related Phases and Intermediate Solvates.

In this study, we systematically investigated the phase diversity and crystallization pathways of the FABr excessive regions of two ternary systems of FABr-PbBr2-DMF and FABr-PbBr2-DMSO (where FA+-formamidinium cations, DMF-dimethylformamide and DMSO-dimethyl sulfoxide solvents). In these systems, a new FA3PbBr5 phase with a structure containing chains of vertex-connected PbBr6 octahedra is discovered, and its crystal structure is refined. We experimentally assess fundamental information on differences in the mechanisms of crystallization process in FABr-PbBr2-DMF and FABr-PbBr2-DMSO systems and determine possible pathways of crystallization of hybrid perovskites. We show that intermediate solvate phases are not observed in the system with DMF solvent, while a number of crystalline solvates tend to form in the system with DMSO at various amounts of FABr excess.

Origin of Free Energy Barriers of Decarboxylation and the Reverse Process of CO2 Capture in Dimethylformamide and in Water.

In aqueous solution, biological decarboxylation reactions proceed irreversibly to completion, whereas the reverse carboxylation processes are typically powered by the hydrolysis of ATP. The exchange of the carboxylate of ring-substituted arylacetates with isotope-labeled CO2 in polar aprotic solvents reported recently suggests a dramatic change in the partition of reaction pathways. Yet, there is little experimental data pertinent to the kinetic barriers for protonation and thermodynamic data on CO2 capture by the carbanions of decarboxylation reactions. Employing a combined quantum mechanical and molecular mechanical simulation approach, we investigated the decarboxylation reactions of a series of organic carboxylate compounds in aqueous and in dimethylformamide solutions, revealing that the reverse carboxylation barriers in solution are fully induced by solvent effects. A linear Bell-Evans-Polanyi relationship was found between the rates of decarboxylation and the Gibbs energies of reaction, indicating diminishing recombination barriers in DMF. In contrast, protonation of the carbanions by the DMF solvent has large free energy barriers, rendering the competing exchange of isotope-labeled CO2 reversible in DMF. The finding of an intricate interplay of carbanion stability and solute-solvent interaction in decarboxylation and carboxylation could be useful to designing novel materials for CO2 capture.

Temperature and solvent exposure response of three fatty acid peroxygenase enzymes for application in industrial enzyme processes.

Free fatty acids (FFAs) are a useful feedstock for a range of industrial chemical synthesis applications. However, efficiently converting FFAs to molecules for biofuel and other high-value chemicals requires more efficient and cost-effective catalysts. Cytochrome P450 fatty acid peroxygenases (CYP152) have a unique chemistry that allows use of the peroxide shunt pathway for biochemical conversion of FFAs. Known CYP152s are heat labile, however, requiring characterization of more thermotolerant versions for use in industrial applications. A fatty acid peroxygenase from Bacillus methanolicus (CYP152K6) was shown here to have a higher optimal reaction temperature than OleT (CYP152L1). CYP152K6 was stable up to 50 °C and showed great stability in 3% acetone and dimethylformamide. Stability in solvents helps the enzyme's substrates remain soluble in solution for more efficient catalysis, and heat stability allows enzymes to remain active longer during industrial processes.

Optical Properties of Composites Based on Poly(o-phenylenediamine), Poly(vinylenefluoride) and Double-Wall Carbon Nanotubes.

In this work, synthesis and optical properties of a new composite based on poly(o-phenylenediamine) (POPD) fiber like structures, poly(vinylidene fluoride) (PVDF) spheres and double-walled carbon nanotubes (DWNTs) are reported. As increasing the PVDF weight in the mixture of the chemical polymerization reaction of o-phenylenediamine, the presence of the PVDF spheres onto the POPD fibers surface is highlighted by scanning electron microscopy (SEM). The down-shift of the Raman line from 1421 cm-1 to 1415 cm-1 proves the covalent functionalization of DWNTs with the POPD-PVDF blends. The changes in the absorbance of the IR bands peaked around 840, 881, 1240 and 1402 cm-1 indicate hindrance steric effects induced of DWNTs to the POPD fiber like structures and the PVDF spheres, as a consequence of the functionalization process of carbon nanotubes with macromolecular compounds. The presence of the PVDF spheres onto the POPD fiber like structures surface induces a POPD photoluminescence (PL) quenching process. An additional PL quenching process of the POPD-PVDF blends is reported to be induced in the presence of DWNTs. The studies of anisotropic PL highlight a change of the angle of the binding of the PVDF spheres onto the POPD fiber like structures surface from 50.2° to 38° when the carbon nanotubes concentration increases in the POPD-PVDF/DWNTs composites mass up to 2 wt.%.

Precise Control of Molecular Self-Diffusion in Isoreticular and Multivariate Metal-Organic Frameworks.

Understanding the factors that affect self-diffusion in isoreticular and multivariate (MTV) MOFs is key to their application in drug delivery, separations, and heterogeneous catalysis. Here, we measure the apparent self-diffusion of solvents saturated within the pores of large single crystals of MOF-5, IRMOF-3 (amino-functionalized MOF-5), and 17 MTV-MOF-5/IRMOF-3 materials at various mole fractions. We find that the apparent self-diffusion coefficient of N,N-dimethylformamide (DMF) may be tuned linearly between the diffusion coefficients of MOF-5 and IRMOF-3 as a function of the linker mole fraction. We compare a series of solvents at saturation in MOF-5 and IRMOF-3 to elucidate the mechanism by which the linker amino groups tune molecular diffusion. The ratio of the self-diffusion coefficients for solvents in MOF-5 to those in IRMOF-3 is similar across all solvents tested, regardless of solvent polarity. We conclude that average pore aperture, not solvent-linker chemical interactions, is the primary factor responsible for the different diffusion dynamics upon introduction of an amino group to the linker.

N-Chlorosuccinimide (NCS)-N,N-dimethylformamide (DMF), a reagent for the oxidation of benzylic alcohols to aldehydes and ketones.

The oxidation of benzylic alcohol to corresponding aldehyde and ketone using N-chlorosuccinimide (NCS)-N,N-dimethylformamide (DMF) has been described. This method gives easy access to the corresponding carbonyl compounds under metal-free conditions, without the use of corrosive reagent at ambient temperature in good yield.

Improved preparation of vitexin from hot water extract of Basella alba, the commercially available vegetable Malabar spinach ("Tsurumurasaki" in Japanese) and the application to semisynthesis of chafuroside B.

Hot water extraction of D-arabinofuranosylvitexin from the raw leaves of commercially available Basella alba "Tsurumurasaki" and subsequent acidic hydrolysis was improved to be a procedure using a high-pressure steam sterilizer to afford vitexin. The amount was estimated to be 14.1 mg from 1 g of dry weight of the raw leaves, whose recovery was calculated to be 95% based on the estimated content of D-arabinofuranosylvitexin in B. alba raw leaves. The product was dehydratively cyclized between hydroxy groups on the carbohydrate and flavone skeletons under modified Mitsunobu reaction conditions in N,N-dimethylformamide to give chafuroside B, which is known to be a bioactive Oolong tea polyphenol. Through these transformations, 10.2 mg of chafuroside B could be semisynthesized from 1 g of dry weight of the raw leaves, and the efficiency was improved compared to that from the extraction from Oolong tea (3.4 µg from 1 g of dry weight).

Co-Culturing of Endothelial and Cancer Cells in a Nanofibrous Scaffold-Based Two-Layer System.

Angiogenesis is critical for local tumor growth. This study aimed to develop a three-dimensional two-layer co-culture system to investigate effects of cancer cells on the growth of endothelial cells (ECs). Poly(ε-caprolactone) (PCL) nanofibrous membranes were generated via electrospinning of PCL in chloroform (C-PCL-M) and chloroform and dimethylformamide (C/DMF-PCL-M). We assembled a two-layer co-culture system using C-PCL-M and C/DMF-PCL-M for EC growth in the upper layer with co-cultured cancer cells in the lower layer. In the absence of vascular endothelial growth factor (VEGF), growth of bEND.3 ECs decreased on C/DMF-PCL-M but not on C-PCL-M with time. Growth of bEND.3 cells on C/DMF-PCL-M was enhanced through co-culturing of CT26 cancer cells and enhanced growth of bEND.3 cells was abrogated with anti-VEGF antibodies and sorafenib. However, EA.hy926 ECs displayed steady growth and proliferation on C/DMF-PCL-M, and their growth was not further increased through co-culturing of cancer cells. Moreover, chemical hypoxia in CT26 cancer cells upon treatment with CoCl2 enhanced the growth of co-cultured bEND.3 cells in the two-layer system. Thus, EC growth on the nanofibrous scaffold is dependent on the types of ECs and composition of nanofibers and this co-culture system can be used to analyze EC growth induced by cancer cells.

Dual Emission in a Ligand and Metal Co-Doped Lanthanide-Organic Framework: Color Tuning and Temperature Dependent Luminescence.

In this study, we report the luminescence color tuning in the lanthanide metal-organic framework (LnMOF) ([La(bpdc)Cl(DMF)] (1); bpdc2- = [1,1'-biphenyl]-4,4'-dicarboxylate, DMF = N,N-dimethylformamide) by introducing dual emission properties in a La3+ MOF scaffold through doping with the blue fluorescent 2,2'-diamino-[1,1'-biphenyl]-4,4'-dicarboxylate (dabpdc2-) and the red emissive Eu3+. With a careful adjustment of the relative doping levels of the lanthanide ions and bridging ligands, the color of the luminescence was modulated, while at the same time the photophysical characteristics of the two chromophores were retained. In addition, the photophysical properties of the parent MOF (1) and its doped counterparts with various dabpdc2-/bpdc2- and Eu3+/La3+ ratios and the photoinduced energy transfer pathways that are possible within these materials are discussed. Finally, the temperature dependence study on the emission profile of a doped analogue containing 10% dabpdc2- and 2.5% Eu3+ (7) is presented, highlighting the potential of this family of materials to behave as temperature sensors.

A Heterometallic Three-Dimensional Metal-Organic Framework Bearing an Unprecedented One-Dimensional Branched-Chain Secondary Building Unit.

A heterometallic metal-organic framework (MOF) of [Cd6Ca4(BTB)6(HCOO)2(DEF)2(H2O)12]∙DEF∙xSol (1, H3BTB = benzene-1,3,5-tribenzoic acid; DEF = N,N'-diethylformamide; xSol. = undefined solvates within the pore) was prepared by solvothermal reaction of Cd(NO3)2·4H2O, CaO and H3BTB in a mixed solvent of DEF/H2O/HNO3. The compatibility of these two divalent cations from different blocks of the periodic table results in a solid-state structure consisting of an unusual combination of a discrete V-shaped heptanuclear cluster of [Cd2Ca]2Ca' and an infinite one-dimensional (1D) chain of [Cd2CaCa']n that are orthogonally linked via a corner-shared Ca2+ ion (denoted as Ca'), giving rise to an unprecedented branched-chain secondary building unit (SBU). These SBUs propagate via tridentate BTB to yield a three-dimensional (3D) structure featuring a corner-truncated P41 helix in MOF 1. This outcome highlights the unique topologies possible via the combination of carefully chosen s- and d-block metal ions with polydentate ligands.

A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase.

N,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the α2 ß2 or (α2 ß2 )2 type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side-chain phenolates and one carboxylate from Glu. The Fe3+ ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.

Cobalt Metallogel Interface for Selectively Sensing l-Tryptophan among Essential Amino Acids.

The development of metallogels widens the span of sensing activity as it opens new opportunities to develop chemosensors through metal-ligand interactions. Herein, a new nitrile-substituted 1,3,5-tricarboxamide-based gelator G4 has been fabricated and shows aggregate-induced enhanced emission (AIEE) after gelation in the presence of water. A dimethylformamide (DMF) solution of the gelator shows rapid crystallization, but addition of water to a DMF solution of gelator G4 leads to gelation at room temperature. In addition, gelator G4 was used for the formation of metallogels, and among them, the cobalt metallogel has been found to be effective for sensing l-tryptophan in the gel state through the quenching of AIEE. Interestingly, the gel is also effective in sensing bovine serum albumin protein at the nanomolar level, which contains an l-tryptophan residue. The limit of detection of Co(II)G4 for selective sensing of tryptophan has been found to be 2.4 × 10-8 M. To the best of our knowledge, there have been no reports to date of a metallogel being utilized to discriminate and selectively sense an amino acid and a protein. The gelation properties of the organic gelator molecule and metallogels have been explored through various spectroscopic tools and physicochemical experiments.

Microcalorimetry and fluorescence show stable peptide nucleic acid (PNA) duplexes in high organic content solvent mixtures.

The selectivity of nucleic acid hybridisation can be exploited to template chemical reactions, enabling materials discovery by chemical evolution. However, to date the range of reactions that can be used has been limited to those that are compatible with aqueous media, since the addition of organic co-solvents can have a large impact on the stability of nucleic acid duplexes. Peptide nucleic acids (PNAs) are promising in this regard because previous studies have suggested they may be stable as duplexes in high organic content solvent mixtures. Here, we use micro-differential scanning calorimetry (micro-DSC) to confirm for the first time that double-stranded PNA (dsPNA) is stable in N,N-dimethylformamide (DMF)/water mixtures up to 95 vol% DMF. Using fluorescence, we corroborate these results and show that the isothermal annealing of PNA in high DMF content solution is also rapid. These findings suggest that PNA could enable the use of a range of water-sensitive chemistries in nucleic acid templating applications.

Regeneration of aged DMF for use in solid-phase peptide synthesis.

Dimethylformamide (DMF), which is still the most commonly used solvent for Fmoc-SPPS, has the potential for degradation over time on exposure to air (and water vapour) and storage, to give dimethylamine and formic acid impurities. In particular, dimethylamine can lead to unwanted deprotection of the fluorenylmethyloxycarbonyl (Fmoc) group during, for example, the initial loading of Fmoc amino acids in SPPS, which leads reduced calculated loading values. We have found that treatment of such aged DMF by simple sparging with an inert gas (N2 ), or vacuum sonication, can regenerate the DMF in order to restore loading levels back to those found for newer, fresh, DMF samples.

An azeotropic drying-free approach for copper-mediated radiofluorination without addition of base.

Copper-mediated radiofluorination provides a quick and versatile approach for 18 F-labeling of arenes and heteroarenes. However, this method is known to be base sensitive, which has been a barrier for preparative scale radiosynthesis. In this report, we provide an approach for copper-mediated radiofluorination without azeotropic drying or adding a base. [18 F]Fluoride trapped on a PS-HCO3 Sep-Pak was quantitatively eluted with a solution of 4-dimethylaminopyridinium trifluoromethanesulfonate (DMAP·OTf) in anhydrous N,N-dimethylformamide (DMF). The eluted solution was directly used for copper-mediated radiofluorination. Twelve boronic ester substrates were tested, yielding fluorinated products in 27% to 83% radiochemical yield based on HPLC analysis. This approach was successfully applied to the radiosynthesis of [18 F]flumazenil, a well-known positron emission tomography (PET) tracer for imaging central benzodiazepine receptors, with a radiochemical yield of 47%. This highly efficient protocol significantly augments the powerful copper-mediated radiofluorination approach.

ON/OFF Photostimulation of Isatin Bipyridyl Hydrazones: Photochemical and Spectral Study.

Four novel isatin hydrazones containing bipyridyl fragments were synthesized as potential ON/OFF switches. Hydrazone Z-isomers exhibit high thermal stability. The characteristic photochemical reaction for all studied hydrazones is the Z-E isomerization in CHCl3. After irradiation of hydrazones 1 and 2 in dimethylformamide (DMF), the photoreaction products are tautomers. When using light with the appropriate wavelength, the photo-tautomerization reaction is reversible. In these conditions, studied hydrazones have ON/OFF switch properties. In the case of hydrazones 1 and 2, by alternating heat and light stimulation it is possible to control the isomerization process reversibly. In the presence of fluoride ions, NH hydrogen from the studied hydrazones is cleaved, and the corresponding anions are formed. The resulting anions of Z-isomers are changed to the corresponding E-isomer at room temperature.

Proton-Dependent Switching of a Novel Amino Chlorin Derivative as a Fluorescent Probe and Photosensitizer for Acidic Media.

A novel chlorin derivative (TPCF20 -NMe2 ) has been synthesized as a syn adduct of a pyrrolidine-fused chlorin bearing a C-linked N,N-dimethylaminophenyl residue. The absorption spectrum of TPCF20 -NMe2 is essentially identical to that of TPCF20 in N,N-dimethylformamide, indicating a very weak interaction between the chlorin macrocycle and the amine group in the ground state. However, the fluorescence emission of the chlorin moiety in TPCF20 -NMe2 is effectively quenched by the attached amine unit. Moreover, TPCF20 -NMe2 is unable to attain a triplet excited state or to photosensitize singlet molecular oxygen. Spectroscopic and redox properties indicate that intramolecular photoinduced electron transfer can take place from the N,N-dimethylaminophenyl group to the chlorin macrocycle. Thus, in an acid medium, protonation of the amino group leads to a considerable increase in the fluorescence emission, triplet excited-state formation, and singlet molecular oxygen production. Photodynamic inactivation of Escherichia coli sensitized by TPCF20 -NMe2 is negligible at neutral pH. However, this chlorin becomes highly effective in inactivating E. coli cells under acidic conditions. Therefore, these results indicate that TPCF20 -NMe2 is an interesting molecular structure, in which protonation of the amino group can be used as an off/on molecular switch activating red fluorescence emission and photodynamic activity capable of eradicating bacteria.

Disulfide-Linked Dendritic Oligomeric Phthalocyanines as Glutathione-Responsive Photosensitizers for Photodynamic Therapy.

A series of disulfide-linked dendritic phthalocyanines were synthesized by using the CuI -catalyzed alkyne-azide cycloaddition reaction as the key step. Whereas these compounds were essentially nonaggregated in N,N-dimethylformamide, they were stacked in citrate solution (pH 7.4, with 1 % Cremophor EL), as shown by the broad appearance of their Q-band absorption. Having two-to-six zinc(II) phthalocyanine units in a molecule, these compounds were significantly self-quenched, particularly in citrate solution. Both the fluorescence intensity and singlet-oxygen generation efficiency were significantly lower than those of the monomeric counterparts, and the self-quenching efficiency increased as the number of phthalocyanine units increased. Upon interaction with 5 mm glutathione (GSH) in citrate solution, the fluorescence intensity of these compounds increased as a result of cleavage of the disulfide linkages and separation of the phthalocyanine units, which thereby reduced the self-quenching effect. The "on/off" ratios were found to be 7, 18, 23, and 21 for the dimeric (PC2), trimeric (PC3), tetrameric (PC4), and hexameric (PC6) systems, respectively. GSH also enhanced the fluorescence emission inside human colon adenocarcinoma HT29 cells and promoted the formation of singlet oxygen of these compounds. Upon irradiation, their half maximal inhibitory concentration (IC50 ) values were found to be in the range of 0.18 to 0.38 µm. Finally, the biodistribution and activation of PC2 and PC6 were also examined in HT29 tumor-bearing nude mice. For both compounds, the fluorescence intensity per unit area at the tumor was found to grow gradually during the first 24 h. Whereas the intensity then dropped for PC2, the intensity for PC6 remained steady over the following 6 d, which might have been a result of the enhanced permeability and retention effect arising from the larger molecular mass of the hexameric system.